Error with the command I used for deblur other

[Mandy]

Hello,
I wanted to use Deblur other for 18S so I could compare the results to DADA2, I'm having a hard time getting the command right, and I always receive the same error. This is the command I used:

qiime deblur denoise-other
--i-demultiplexed-seqs demux-filtered.qza \
--i-reference-seqs 99_otus_18S.qza
--p-trim-length 244
--o-representative-sequences rep-seqs-deblur.qza
--o-table table-deblur.qza
--p-sample-stats
--o-stats deblur-stats.qza
--p-jobs-to-start 8
--output-dir Deblur_denoise_output
--verbose

and this is the error that occurs: (1/6) Missing option "--i-reference-seqs".
(2/6) Missing option "--p-trim-length".
(3/6) Missing option "--o-table". ("--output-dir" may also be used)
(4/6) Missing option "--o-representative-sequences". ("--output-dir" may
also be used)
(5/6) Missing option "--o-stats". ("--output-dir" may also be used)
(6/6) Got unexpected extra argument ( )
[cb761009@login.lcc2 18S]$ --i-reference-seqs 99_otus_18S.qza \

--p-trim-length 244
--o-representative-sequences rep-seqs-deblur.qza
--o-table table-deblur.qza
--p-sample-stats
--o-stats deblur-stats.qza
-bash: --i-reference-seqs: command not found
[cb761009@login.lcc2 18S] --p-jobs-to-start 8 -bash: --p-jobs-to-start: command not found [cb761009@login.lcc2 18S] --output-dir Deblur_denoise_output
-bash: --output-dir: command not found
[cb761009@login.lcc2 18S]$ --verbose
-bash: --verbose: command not found

thank you in advance for any help!!

[llenzi (Luca)]

Hi @Mandy,

Welcome in the forum!

If you work in bash, to run a command on multiple lines you have to add the '' (backslash) sign at the end of each line, so bash knows it has to interpret all as one big chunk of command.

Hope it make sense!
Luca

[Mandy]

thank you for your immediate reply!
that makes perfect sense, but sadly I still receive the same error, even after adding the backslash sign at the end of every line..

kind regards

[llenzi (Luca)]

Hi @Mandy,

Can I ask you how you are running the command?
Copy and paste from a text editor, or writing in bash directly?

Just to double check, at the start of the option do you have a double '- -' or a long trait as in the command above?

Cheers

[Mandy]

Yes, I write my commands in Word and copy paste them! I can try writing it out myself, I usually don’t do that to avoid mistakes.
They have a double ‘ - - ‘
The only thing that I have not yet tried to change, is the reference-seqs I use, which is a SILVA database that I’ve been using for all of my 16S research. I couldn’t find a lot of information on what Ref-seqs you’re supposed to use for deblur other, so maybe my mistake (Or at least one of them) lies there?

Thanks again for your help!

[llenzi (Luca)]

Hi Mandy,

I suspect there are few invisible characters from Word that are messing things up. Please, try to copy-and-paste first on notepad (TextEdit if you are on Mac) so it will be cleaned, then copy-paste again on bash.

Cheers

[Mandy]

Hi again,
I did as you suggested and was met with a new error this time: Error: QIIME 2 plugin 'deblur' has no action 'denoise'. (Possible commands: denoise-16S, denoise-other)

So I changed "deblur denoise-other" to "denoise-other" which was met with a similar error: Error: QIIME 2 has no plugin/command named 'denoise-other'.

what am I missing?
thanks!

[llenzi (Luca)]

Hi,

I think you were right the first time, the command is 'deblur denoise-other' (as in denoise-other: Deblur sequences using a user-specified positive filter. — QIIME 2 2020.6.0 documentation)

I think there is still some odd invisible character passed to the terminal. Could you test if typing from scratch would works? (at least tying 'qiime deblur denoise-other' to get the help)

Cheers

[Mandy]

hello,

wanted to let you know that I typed the command out this time, but like this:

qiime deblur denoise-other --i-demultiplexed-seqs demux-filtered.qza --i-reference-seqs 99_otus_18S.qza --p-trim-length 244 --o-representative-sequences rep-seqs-deblur.qza --o-table table-deblur.qza --p-sample-stats --o-stats deblur-stats.qza

and it worked!! thanks again for your time and help.

[ben (benjamin w.)]

@Mandy

After every new line there should be a \

It tells the terminal prompt to go to the next line in the command. Your initial command:

qiime deblur denoise-other
–i-demultiplexed-seqs demux-filtered.qza
–i-reference-seqs 99_otus_18S.qza
–p-trim-length 244
–o-representative-sequences rep-seqs-deblur.qza
–o-table table-deblur.qza
–p-sample-stats
–o-stats deblur-stats.qza
–p-jobs-to-start 8
–output-dir Deblur_denoise_output
–verbose

Needed to be written:

qiime deblur denoise-other \
–i-demultiplexed-seqs demux-filtered.qza \
–i-reference-seqs 99_otus_18S.qza \
–p-trim-length 244 \
–o-representative-sequences rep-seqs-deblur.qza \
–o-table table-deblur.qza \
–p-sample-stats \
–o-stats deblur-stats.qza \
–p-jobs-to-start 8 \
–output-dir Deblur_denoise_output \
–verbose

Notice that without the last \ it ends the commands.

Ben

[Mandy]

Hi Ben, thanks for your input! I already tried that, that didn’t make a difference. But earlier I replied that I typed the command out myself and It worked, so already solved the problem! Thank you though.
Cheers!